Mercurial > repos > lecorguille > xcms_retcor
changeset 1:f42bd3de6aad draft
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--- a/Makefile Fri Aug 07 05:34:26 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,23 +0,0 @@ -# USAGE: make [install|clean] - -# -------- VARIABLE -------- - -OBJ=xcms_retcor.tgz -DEP=abims_xcms_retcor.xml tool_dependencies.xml repository_dependencies.xml static test-data - - -# ------------------------ - -all: $(OBJ) - -$(OBJ): $(DEP) - tar --exclude=".svn" -zchf $@ $^ - -# ------------------------ - -install: $(OBJ) - mv *.tgz ~ - -clean: - rm *.tgz -
--- a/abims_xcms_retcor.xml Fri Aug 07 05:34:26 2015 -0400 +++ b/abims_xcms_retcor.xml Fri Jan 08 09:52:38 2016 -0500 @@ -1,4 +1,4 @@ -<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.2"> +<tool id="abims_xcms_retcor" name="xcms.retcor" version="2.0.4"> <description>Retention Time Correction using retcor function from xcms R package </description> @@ -13,9 +13,17 @@ <exit_code range="1:" level="fatal" /> </stdio> - <command> + <command><![CDATA[ xcms.r - image $image xfunction retcor method $methods.method + image $image + xfunction retcor + + xsetRdataOutput $xsetRData + ticspdf $ticsCorPdf + bicspdf $bpcsCorPdf + rplotspdf $rplotsPdf + + method $methods.method #if $methods.method == "obiwarp": profStep $methods.profStep #else @@ -28,13 +36,16 @@ plottype $methods.options.plottype #end if #end if - && ( mv retcor.RData $xsetRData; - mv TICs_corrected.pdf $ticsCorPdf ; - mv BPCs_corrected.pdf $bpcsCorPdf ; - mv Rplots.pdf $rplotsPdf 2> /dev/null); - cat xset.log; + #if $zip_file: + zipfile $zip_file + #end if + ; + return=\$?; + mv log.txt $log; + cat $log; + sh -c "exit \$return" - </command> + ]]></command> <inputs> <param name="image" type="data" format="rdata.xcms.raw,rdata.xcms.group,rdata" label="xset RData file" help="output file from another function xcms (xcmsSet, retcor etc.)" /> @@ -61,22 +72,24 @@ <when value="show"> <param name="span" type="float" value="0.2" label="Degree of smoothing for local polynomial regression fitting" help="[span]"/> - <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal"> - <option value="gaussian" selected="true">gaussian</option> - <option value="symmetric">symmetric</option> - </param> + <param name="family" type="select" label="Family" help="[family] if gaussian fitting is by least-squares with no outlier removal, and if symmetric a re descending M estimator is used with Tukey's biweight function, allowing outlier removal"> + <option value="gaussian" selected="true">gaussian</option> + <option value="symmetric">symmetric</option> + </param> - <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density"> + <param name="plottype" type="select" help="[plottype] if deviation plot retention time deviation points and regression fit, and if mdevden also plot peak overall peak density and retention time correction peak density"> <option value="none" selected="true">none</option> <option value="deviation">deviation</option> <option value="mdevden">mdevden</option> </param> </when> - <when value="hide"> - </when> + <when value="hide"> + </when> </conditional> </when> </conditional> + <!-- To pass planemo test --> + <param name="zip_file" type="hidden_data" format="no_unzip.zip" label="Zip file" /> </inputs> <outputs> @@ -89,6 +102,7 @@ </data> <data name="ticsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.TICs_corrected.pdf" /> <data name="bpcsCorPdf" format="pdf" label="${image.name[:-6]}.retcor.BPCs_corrected.pdf" /> + <data name="log" format="txt" label="xset.log.txt" hidden="true" /> </outputs> <tests> @@ -102,14 +116,25 @@ <param name="methods.options.span" value="0.2"/> <param name="methods.options.family" value="gaussian"/> <param name="methods.options.plottype" value="deviation"/> - <output name="xsetRData" file="xset.group.retcor.RData" /> - <output name="rplotsPdf" file="xset.group.retcor.Rplots.pdf" /> - <output name="ticsCorPdf" file="xset.group.retcor.TICs_corrected.pdf" /> - <output name="bpcsCorPdf" file="xset.group.retcor.BPCs_corrected.pdf" /> + <param name="zip_file" value="sacuri.zip"/> + <!--<output name="xsetRData" file="xset.group.retcor.RData" />--> + <!--<output name="rplotsPdf" file="xset.group.retcor.Rplots.pdf" />--> + <!--<output name="ticsCorPdf" file="xset.group.retcor.TICs_corrected.pdf" />--> + <!--<output name="bpcsCorPdf" file="xset.group.retcor.BPCs_corrected.pdf" />--> + <output name="log"> + <assert_contents> + <has_text text="object with 9 samples" /> + <has_text text="Time range: 0.7-1139.9 seconds (0-19 minutes)" /> + <has_text text="Mass range: 50.0019-999.9863 m/z" /> + <has_text text="Peaks: 135846 (about 15094 per sample)" /> + <has_text text="Peak Groups: 0" /> + <has_text text="Sample classes: bio, blank" /> + </assert_contents> + </output> </test> </tests> - <help> + <help><![CDATA[ .. class:: infomark @@ -266,7 +291,7 @@ .. image:: xcms_retcor.png - </help> + ]]></help> <citations> <citation type="doi">10.1021/ac051437y</citation>
--- a/planemo.sh Fri Aug 07 05:34:26 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,1 +0,0 @@ -planemo shed_init -f --name=xcms_retcor --owner=lecorguille --description="[W4M][GC-MS] XCMS R Package - Preprocessing - Correct retention time from different samples" --homepage_url="http://workflow4metabolomics.org" --long_description="Part of the W4M project: http://workflow4metabolomics.org\n\nXCMS: http://www.bioconductor.org/packages/release/bioc/html/xcms.html\n\nRetention Time Correction using retcor function from xcms R package\n\nBEWARE: this tool don't come with its script. You will need to install the dedicated package_xcms_w4m_script too" --category="Metabolomics"
--- a/repository_dependencies.xml Fri Aug 07 05:34:26 2015 -0400 +++ b/repository_dependencies.xml Fri Jan 08 09:52:38 2016 -0500 @@ -1,5 +1,5 @@ <?xml version="1.0"?> <repositories> - <repository changeset_revision="9ed593071db2" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="5527da68412e" name="no_unzip_datatype" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" /> <repository changeset_revision="bff835d58914" name="rdata_xcms_datatypes" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/.svn/entries Fri Jan 08 09:52:38 2016 -0500 @@ -0,0 +1,31 @@ +10 + +dir +157 +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo/xcms_retcor/static +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo + + + +2015-06-08T08:49:50.776281Z +104 +mmonsoor + + + + + + + + + + + + + + +87d02074-be8c-4456-a071-04b64888326c + +images +dir +
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/images/.svn/prop-base/xcms_retcor.png.svn-base Fri Jan 08 09:52:38 2016 -0500 @@ -0,0 +1,9 @@ +K 14 +svn:executable +V 1 +* +K 13 +svn:mime-type +V 24 +application/octet-stream +END
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/images/.svn/prop-base/xcms_retcor_workflow.png.svn-base Fri Jan 08 09:52:38 2016 -0500 @@ -0,0 +1,9 @@ +K 14 +svn:executable +V 1 +* +K 13 +svn:mime-type +V 24 +application/octet-stream +END
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/.svn/entries Fri Jan 08 09:52:38 2016 -0500 @@ -0,0 +1,198 @@ +10 + +dir +157 +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo/xcms_retcor/test-data +svn+ssh://lecorguille@svn.sb-roscoff.fr/svn/logiciel/galaxy-workflow4metabo + + + +2015-08-03T13:28:59.062143Z +155 +lecorguille + + + + + + + + + + + + + + +87d02074-be8c-4456-a071-04b64888326c + +xset.group.retcor.BPCs_corrected.pdf +file + + + + +2015-08-03T13:03:57.000000Z +d9d83e17ff0b99f220fca6d9a6ced3df +2015-08-03T13:28:59.062143Z +155 +lecorguille +has-props + + + + + + + + + + + + + + + + + + + + +99861 + +xset.group.retcor.RData +file + + + + +2015-08-03T13:03:22.000000Z +62b168526bed180836d55116836b51b4 +2015-08-03T13:28:59.062143Z +155 +lecorguille +has-props + + + + + + + + + + + + + + + + + + + + +7946811 + +xset.group.retcor.Rplots.pdf +file + + + + +2015-08-03T13:03:34.000000Z +edd0b128ea7c3494dbae5f76dcf99d92 +2015-08-03T13:28:59.062143Z +155 +lecorguille + + + + + + + + + + + + + + + + + + + + + +121054 + +xset.group.RData +file + + + + +2015-08-03T13:02:45.000000Z +831e1e463e0d0689d7e109cf5892f5a7 +2015-08-03T13:28:59.062143Z +155 +lecorguille +has-props + + + + + + + + + + + + + + + + + + + + +8031328 + +xset.group.retcor.TICs_corrected.pdf +file + + + + +2015-08-03T13:03:47.000000Z +8d4083a5d0888df2aba778f95952a4b8 +2015-08-03T13:28:59.062143Z +155 +lecorguille + + + + + + + + + + + + + + + + + + + + + +101732 +
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/.svn/prop-base/xset.group.RData.svn-base Fri Jan 08 09:52:38 2016 -0500 @@ -0,0 +1,5 @@ +K 13 +svn:mime-type +V 24 +application/octet-stream +END
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/.svn/prop-base/xset.group.retcor.BPCs_corrected.pdf.svn-base Fri Jan 08 09:52:38 2016 -0500 @@ -0,0 +1,5 @@ +K 13 +svn:mime-type +V 24 +application/octet-stream +END
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/.svn/prop-base/xset.group.retcor.RData.svn-base Fri Jan 08 09:52:38 2016 -0500 @@ -0,0 +1,5 @@ +K 13 +svn:mime-type +V 24 +application/octet-stream +END
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/log.txt Fri Jan 08 09:52:38 2016 -0500 @@ -0,0 +1,52 @@ + PACKAGE INFO +parallel 3.1.2 +BiocGenerics 0.14.0 +Biobase 2.28.0 +Rcpp 0.12.0 +mzR 2.2.2 +xcms 1.44.0 +snow 0.3.13 +batch 1.1.4 + + + ARGUMENTS INFO +image test-data/xset.group.RData +xfunction retcor +xsetRdataOutput test-data/xset.group.retcor.RData +ticspdf xset.group.retcor.TICs_corrected.pdf +bicspdf xset.group.retcor.BPCs_corrected.pdf +rplotspdf xset.group.retcor.Rplots.pdf +method obiwarp +profStep 1 +zipfile test-data/sacuri.zip + + + INFILE PROCESSING INFO + + + ARGUMENTS PROCESSING INFO + + + MAIN PROCESSING INFO +center sample: HU_neg_060 +Processing: HU_neg_028 HU_neg_051 HU_neg_017 HU_neg_034 Blanc09 Blanc06 Blanc12 Blanc04 +null device + 1 + + + XSET OBJECT INFO +An "xcmsSet" object with 9 samples + +Time range: 0.7-1139.9 seconds (0-19 minutes) +Mass range: 50.0019-999.9863 m/z +Peaks: 135846 (about 15094 per sample) +Peak Groups: 0 +Sample classes: bio, blank + +Profile settings: method = bin + step = 0.01 + +Memory usage: 13.8 MB + + + DONE
--- a/tool_dependencies.xml Fri Aug 07 05:34:26 2015 -0400 +++ b/tool_dependencies.xml Fri Jan 08 09:52:38 2016 -0500 @@ -1,12 +1,12 @@ <?xml version="1.0"?> <tool_dependency> <package name="R" version="3.1.2"> - <repository changeset_revision="41f43a2064ba" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="1ca39eb16186" name="package_r_3_1_2" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="xcms" version="1.44.0"> - <repository changeset_revision="709473976109" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="8ea252413ed6" name="package_r_xcms_1_44_0" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> <package name="xcms_w4m_script" version="2.1"> - <repository changeset_revision="af163ca0ac33" name="package_xcms_w4m_script_2_1" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="745fc3cb412e" name="package_xcms_w4m_script_2_1" owner="lecorguille" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </package> </tool_dependency>